The objectives of the present study were to evaluate genotypic potential among various sorghum genotypes through effective and quick screening methods for salt tolerance and to develop reliable, efficient and rapid screening criteria for sorghum germplasm through conventional germination process, physiological, biochemical and latest RAPD and ISSR techniques. For this purpose fifty sorghum genotypes were screened for 100 mM NaCl salinity stress in Petri plates for 14 days and seven best performing genotypes (JS-2002, JS-263, Hegari- sorghum, PSV-4, Sandalbar, Noor and FJ-115) were selected for further evaluation through different physiological indices used as screening tools under 50, 100, 150 and 200 mM NaCl levels. Four genotypes consisted of two tolerant and two sensitive were selected to investigate the traits variations in growth and yield, physiological and biochemical markers in sand culture experiments. These genotypes were also subjected for RAPD and ISSR analyses to identify DNA markers in sorghum germplasm for salt tolerance. The whole studies were conducted in three different phases: In the first phase, influence of salinity was investigated on germination and seedling growth which was negatively affected by salinity stress in all tested sorghum genotypes. The germination percentage, stress tolerance indices for germination, shoot length, root length, shoot and root fresh weights shoot and root dry weights were also negatively affected by the different levels of NaCl in all the seven genotypes of sorghum. The two genotypes (JS-2002 and Sandalbar) showed the best performance at all levels of salt stress were designated as tolerant and the two poor performing (Noor and FJ-115) as sensitive. These four genotypes were used further to study the biochemical, physiological, and RAPD and ISSR markers. In second phase salinity induced changes in agronomic attributes were estimated and results clearly indicated that all these parameters were adversely affected by salt stress in all four tested sorghum genotypes. All agronomic traits like plant height (18%), root length (5%), fresh weights of roots (47%), dry weights of roots (24%), fresh weights of shoots (24.5%) and dry weights of shoots (23%) reduced significantly at 100 mM NaCl in all four sorghum genotypes. Similarly physiological parameters like water potential, osmotic potential, turgor potential, transpiration rate, net rate of photosynthesis and stomatal conductance were also adversely affected by salinity in all sorghum genotypes. The photosynthetic pigments like chlorophyll “a” (29%), chlorophyll “b” (54%) and total chlorophyll (38%) were also reduced due to salinity stress. While an increase in total soluble sugars (49%), sub-stomatal conductance (18%), carotenoids (46%) have been recoded in four sorghum genotypes under saline conditions. Nitrogen metabolism was adversely affected by salinity in all four sorghum genotypes by reducing total nitrogen (52%), proteins (34%), nitrate reductase activity (13%), leaf nitrate (54%). However, accumulation of total free amino acids (37%) in salt stressed plants was higher than those growing under normal conditions. Same was the case with the accumulation of Na+ and chloride. While reduction in shoot K+ (32%) and root K+ (34%), shoot P (22%) root P (38%), shoot Ca2+ (34%), root Ca2+ (25%), shoot Mg2+ (40%) and root Mg2+ (54%) has been recorded in plants grown under saline conditions. It was noted that antioxidants activity e.g. SOD and POD have also been severely inhibited in salinity stressed plants of all sorghum genotypes. However, catalase activity was enhanced in plants growing under salinity stress than that which were growing in normal conditions. However, all yield parameters were adversely affected in plants exposed to salt stress environment. Number of panicles per plant (29%), weight of grains per panicle (40%), 1000 grain weight (37%), and grain yield per plant (57%) were significantly reduced in plants growing in saline conditions. In third phase, RAPD and ISSR marker analysis was conducted and specific markers for salt tolerance were identified in sorghum germplasm. The 20 different primers (10 RAPD and 10 ISSR) expressed different levels of polymorphism, ranging from 0.0% with RAPD C02 to 100% with RAPD primer O09 and O16. Only RAPD primer C02 was monomorphic, while all other RAPD and ISSR primers were polymorphic and these primers showed 47% of polymorphism in four genotypes of sorghum. The lowest number of DNA fragments were amplified by RAPD primer O09 (4 bands) and maximum number of bands (13 bands) were developed by ISSR primer HB11 and HB12. Both RAPD and ISSR primers identified total 21 positive and 10 negative markers for salt tolerance in four sorghum genotypes. Both RAPD (C05, C16, O09) and ISSR primers (17898A, 17899B, HB11) might be used to distinguish salt tolerant genotypes from salt sensitive genotypes in sorghum germplasm. The ISSR primer 17898A is the best to distinguish the sorghum genotypes for salt tolerance. The dendrogram obtained on the basis of data by RAPD and ISSR analysis divided four genotypes in to two different clusters supported that Sandalbar and JS- 2002 are similar to each other and placed in the same group while, Noor and FJ-115 are present in another cluster. These identified molecular markers are useful in selecting the true salt tolerant sorghum genotypes. This molecular approach would also enable the biotechnologists to select the promising lines because selection is based on DNA markers rather than phenotypic traits which are influenced by the environmental stresses. The results of the present study revealed that RAPD and ISSR analysis is an effective tool to detect polymorphism between salt tolerant and sensitive sorghum genotypes thus will speed up the screening of salt tolerant genotypes and eventually help breeders in developing the salt tolerant varieties or in selection of salt tolerant germplasm of sorghum.